VSEPR method consists a set of simple rules based on the results of quantum-chemical calculations - hence you get electronic configuation around examined atom (from main groups of elements ie s and p blocks) firstly. This configuration is very often considered as hybridization of atom eg. sp2, dsp3 and so on. Since electron pairs or single electrons show small volumes in relation to atoms or substituents, for physical shape of molecule (you call it - geometry shape) they are neglected.
The description AXNEZ gives you information about N+Z directions where electrons (bonded or nonbonded) around atom A can be found. The arrangement of electrons and substituents should minimize energy of repulsion (rules 120 and 90 degrees).
An that is all. You should memmorize a few basic shapes, and angle rules - then you can predict real shape almost all molecules with A atom coming from s or p block of elements (almost all because this is a simple set of rules, but not a general theory).